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van Huizen M, Bloeme - ter Horst JR, de Gruyter HLM, Geurink PP, van der Heden van Noort GJ, Knaap RCM, Nelemans T, Ogando NS, Leijs AA, Urakova N, Mark BL, Snijder EJ, Myeni SK, Kikkert M. Deubiquitinating activity of SARS-CoV-2 papain-like protease does not influence virus replication or innate immune responses in vivo. PLoS Pathog 2024; 20:e1012100. [PMID: 38527094 PMCID: PMC10994560 DOI: 10.1371/journal.ppat.1012100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/04/2024] [Accepted: 03/04/2024] [Indexed: 03/27/2024] Open
Abstract
The coronavirus papain-like protease (PLpro) is crucial for viral replicase polyprotein processing. Additionally, PLpro can subvert host defense mechanisms by its deubiquitinating (DUB) and deISGylating activities. To elucidate the role of these activities during SARS-CoV-2 infection, we introduced mutations that disrupt binding of PLpro to ubiquitin or ISG15. We identified several mutations that strongly reduced DUB activity of PLpro, without affecting viral polyprotein processing. In contrast, mutations that abrogated deISGylating activity also hampered viral polyprotein processing and when introduced into the virus these mutants were not viable. SARS-CoV-2 mutants exhibiting reduced DUB activity elicited a stronger interferon response in human lung cells. In a mouse model of severe disease, disruption of PLpro DUB activity did not affect lethality, virus replication, or innate immune responses in the lungs. This suggests that the DUB activity of SARS-CoV-2 PLpro is dispensable for virus replication and does not affect innate immune responses in vivo. Interestingly, the DUB mutant of SARS-CoV replicated to slightly lower titers in mice and elicited a diminished immune response early in infection, although lethality was unaffected. We previously showed that a MERS-CoV mutant deficient in DUB and deISGylating activity was strongly attenuated in mice. Here, we demonstrate that the role of PLpro DUB activity during infection can vary considerably between highly pathogenic coronaviruses. Therefore, careful considerations should be taken when developing pan-coronavirus antiviral strategies targeting PLpro.
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Affiliation(s)
- Mariska van Huizen
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Jonna R. Bloeme - ter Horst
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Heidi L. M. de Gruyter
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Paul P. Geurink
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Centre, Leiden, The Netherlands
| | - Gerbrand J. van der Heden van Noort
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Centre, Leiden, The Netherlands
| | - Robert C. M. Knaap
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Tessa Nelemans
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Natacha S. Ogando
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Anouk A. Leijs
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Nadya Urakova
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Brian L. Mark
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Eric J. Snijder
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Sebenzile K. Myeni
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Marjolein Kikkert
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
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Bailey-Elkin BA, Knaap RCM, De Silva A, Boekhoud IM, Mous S, van Vught N, Khajehpour M, van den Born E, Kikkert M, Mark BL. Demonstrating the importance of porcine reproductive and respiratory syndrome virus papain-like protease 2 deubiquitinating activity in viral replication by structure-guided mutagenesis. PLoS Pathog 2023; 19:e1011872. [PMID: 38096325 PMCID: PMC10754444 DOI: 10.1371/journal.ppat.1011872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 12/28/2023] [Accepted: 11/28/2023] [Indexed: 12/29/2023] Open
Abstract
Deubiquitination of cellular substrates by viral proteases is a mechanism used to interfere with host cellular signaling processes, shared between members of the coronavirus- and arterivirus families. In the case of Arteriviruses, deubiquitinating and polyprotein processing activities are accomplished by the virus-encoded papain-like protease 2 (PLP2). Several studies have implicated the deubiquitinating activity of the porcine reproductive and respiratory syndrome virus (PRRSV) PLP2 in the downregulation of cellular interferon production, however to date, the only arterivirus PLP2 structure described is that of equine arteritis virus (EAV), a distantly related virus. Here we describe the first crystal structure of the PRRSV PLP2 domain both in the presence and absence of its ubiquitin substrate, which reveals unique structural differences in this viral domain compared to PLP2 from EAV. To probe the role of PRRSV PLP2 deubiquitinating activity in host immune evasion, we selectively removed this activity from the domain by mutagenesis and found that the viral domain could no longer downregulate cellular interferon production. Interestingly, unlike EAV, and also unlike the situation for MERS-CoV, we found that recombinant PRRSV carrying PLP2 DUB-specific mutations faces significant selective pressure to revert to wild-type virus in MARC-145 cells, suggesting that the PLP2 DUB activity, which in PRRSV is present as three different versions of viral protein nsp2 expressed during infection, is critically important for PRRSV replication.
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Affiliation(s)
- Ben A. Bailey-Elkin
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Robert C. M. Knaap
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, The Netherlands
| | - Anuradha De Silva
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ilse M. Boekhoud
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, The Netherlands
| | - Sandra Mous
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, The Netherlands
| | - Niek van Vught
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, The Netherlands
| | - Mazdak Khajehpour
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Marjolein Kikkert
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, The Netherlands
| | - Brian L. Mark
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
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Bailey-Elkin BA, Knaap RCM, Kikkert M, Mark BL. Structure and Function of Viral Deubiquitinating Enzymes. J Mol Biol 2017; 429:3441-3470. [PMID: 28625850 PMCID: PMC7094624 DOI: 10.1016/j.jmb.2017.06.010] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 06/12/2017] [Accepted: 06/13/2017] [Indexed: 01/12/2023]
Abstract
Post-translational modification of cellular proteins by ubiquitin regulates numerous cellular processes, including innate and adaptive immune responses. Ubiquitin-mediated control over these processes can be reversed by cellular deubiquitinating enzymes (DUBs), which remove ubiquitin from cellular targets and depolymerize polyubiquitin chains. The importance of protein ubiquitination to host immunity has been underscored by the discovery of viruses that encode proteases with deubiquitinating activity, many of which have been demonstrated to actively corrupt cellular ubiquitin-dependent processes to suppress innate antiviral responses and promote viral replication. DUBs have now been identified in diverse viral lineages, and their characterization is providing valuable insights into virus biology and the role of the ubiquitin system in host antiviral mechanisms. Here, we provide an overview of the structural biology of these fascinating viral enzymes and their role innate immune evasion and viral replication.
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Affiliation(s)
- Ben A Bailey-Elkin
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - Robert C M Knaap
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Marjolein Kikkert
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Brian L Mark
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada.
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Zhang W, Bailey-Elkin BA, Knaap RCM, Khare B, Dalebout TJ, Johnson GG, van Kasteren PB, McLeish NJ, Gu J, He W, Kikkert M, Mark BL, Sidhu SS. Potent and selective inhibition of pathogenic viruses by engineered ubiquitin variants. PLoS Pathog 2017; 13:e1006372. [PMID: 28542609 PMCID: PMC5451084 DOI: 10.1371/journal.ppat.1006372] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 05/31/2017] [Accepted: 04/23/2017] [Indexed: 12/20/2022] Open
Abstract
The recent Middle East respiratory syndrome coronavirus (MERS-CoV), Ebola and Zika virus outbreaks exemplify the continued threat of (re-)emerging viruses to human health, and our inability to rapidly develop effective therapeutic countermeasures. Many viruses, including MERS-CoV and the Crimean-Congo hemorrhagic fever virus (CCHFV) encode deubiquitinating (DUB) enzymes that are critical for viral replication and pathogenicity. They bind and remove ubiquitin (Ub) and interferon stimulated gene 15 (ISG15) from cellular proteins to suppress host antiviral innate immune responses. A variety of viral DUBs (vDUBs), including the MERS-CoV papain-like protease, are responsible for cleaving the viral replicase polyproteins during replication, and are thereby critical components of the viral replication cycle. Together, this makes vDUBs highly attractive antiviral drug targets. However, structural similarity between the catalytic cores of vDUBs and human DUBs complicates the development of selective small molecule vDUB inhibitors. We have thus developed an alternative strategy to target the vDUB activity through a rational protein design approach. Here, we report the use of phage-displayed ubiquitin variant (UbV) libraries to rapidly identify potent and highly selective protein-based inhibitors targeting the DUB domains of MERS-CoV and CCHFV. UbVs bound the vDUBs with high affinity and specificity to inhibit deubiquitination, deISGylation and in the case of MERS-CoV also viral replicative polyprotein processing. Co-crystallization studies further revealed critical molecular interactions between UbVs and MERS-CoV or CCHFV vDUBs, accounting for the observed binding specificity and high affinity. Finally, expression of UbVs during MERS-CoV infection reduced infectious progeny titers by more than four orders of magnitude, demonstrating the remarkable potency of UbVs as antiviral agents. Our results thereby establish a strategy to produce protein-based inhibitors that could protect against a diverse range of viruses by providing UbVs via mRNA or protein delivery technologies or through transgenic techniques. Emerging viruses pose a tremendous challenge to human health. While vaccine-based approaches are desirable in terms of infection prevention in the longer term, alternative antiviral strategies are needed, especially when providing treatment options for infected patients during acute outbreaks. Here we applied protein engineering technology to target virus-encoded deubiquitinating enzymes of two viruses with significant impact on human health: Middle East respiratory syndrome coronavirus (MERS-CoV) and Crimean-Congo hemorrhagic fever virus (CCHFV). This resulted in the rapid identification of ubiquitin variant (UbV) inhibitors that bound with high affinity and specificity to the viral deubiquitinating enzymes. These proteins inhibited the catalytic activities of the deubiquitinating enzymes and almost completely blocked MERS-CoV infection. This work provides proof-of-principle that structurally diverse, virus-specific deubiquitinating enzymes can be selectively targeted through rational protein design technology, and therefore opens new avenues for quickly developed molecularly tailored therapy across a broad spectrum of viral pathogens that infect humans, livestock and plants.
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Affiliation(s)
- Wei Zhang
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Ben A. Bailey-Elkin
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Robert C. M. Knaap
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Baldeep Khare
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Tim J. Dalebout
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Garrett G. Johnson
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Puck B. van Kasteren
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Nigel J. McLeish
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jun Gu
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Wenguang He
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Marjolein Kikkert
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
- * E-mail: (MK); (BLM); (SSS)
| | - Brian L. Mark
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- * E-mail: (MK); (BLM); (SSS)
| | - Sachdev S. Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- * E-mail: (MK); (BLM); (SSS)
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van Kasteren PB, Knaap RCM, van den Elzen P, Snijder EJ, Balasuriya UBR, van den Born E, Kikkert M. In vivo assessment of equine arteritis virus vaccine improvement by disabling the deubiquitinase activity of papain-like protease 2. Vet Microbiol 2015; 178:132-7. [PMID: 25975520 PMCID: PMC7117436 DOI: 10.1016/j.vetmic.2015.04.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 04/03/2015] [Accepted: 04/20/2015] [Indexed: 11/21/2022]
Abstract
Equine arteritis virus lacking PLP2 DUB activity is replication competent in vivo. EAV lacking PLP2 DUB activity protects against challenge with KY84 virus. An enhanced immune response was not detected using this experimental set-up.
Arteriviruses are a family of positive-stranded RNA viruses that includes the prototypic equine arteritis virus (EAV) and porcine reproductive and respiratory syndrome virus (PRRSV). Although several vaccines against these viruses are commercially available there is room for improvement, especially in the case of PRRSV. The ability of arteriviruses to counteract the immune response is thought to decrease the efficacy of the current modified live virus vaccines. We have recently shown that the deubiquitinase (DUB) activity of EAV papain-like protease 2 (PLP2) is important for the inhibition of innate immune activation during infection. A vaccine virus lacking PLP2 DUB activity may therefore be more immunogenic and provide improved protection against subsequent challenge than its DUB-competent counterpart. To test this hypothesis, twenty Shetland mares were randomly assigned to one of three groups. Two groups were vaccinated, either with DUB-positive (n = 9) or DUB-negative (n = 9) recombinant EAV. The third group (n = 2) was not vaccinated. All horses were subsequently challenged with the virulent KY84 strain of EAV. Both vaccine viruses proved to be replication competent in vivo. In addition, the DUB-negative virus provided a similar degree of protection against clinical disease as its DUB-positive parental counterpart. Owing to the already high level of protection provided by the parental virus, a possible improvement due to inactivation of PLP2 DUB activity could not be detected under these experimental conditions. Taken together, the data obtained in this study warrant further in vivo investigations into the potential of using DUB-mutant viruses for the improvement of arterivirus vaccines.
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Affiliation(s)
- Puck B van Kasteren
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Robert C M Knaap
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Paul van den Elzen
- MSD Animal Health, Wim de Körverstraat 35, 5831 AN Boxmeer, The Netherlands
| | - Eric J Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Udeni B R Balasuriya
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, 1400 Nicholasville Road, 40546-0099 Lexington, KY, USA
| | - Erwin van den Born
- MSD Animal Health, Wim de Körverstraat 35, 5831 AN Boxmeer, The Netherlands
| | - Marjolein Kikkert
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands.
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Bailey-Elkin BA, Knaap RCM, Johnson GG, Dalebout TJ, Ninaber DK, van Kasteren PB, Bredenbeek PJ, Snijder EJ, Kikkert M, Mark BL. Crystal structure of the Middle East respiratory syndrome coronavirus (MERS-CoV) papain-like protease bound to ubiquitin facilitates targeted disruption of deubiquitinating activity to demonstrate its role in innate immune suppression. J Biol Chem 2014; 289:34667-82. [PMID: 25320088 PMCID: PMC4263872 DOI: 10.1074/jbc.m114.609644] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) is a newly emerging human
pathogen that was first isolated in 2012. MERS-CoV replication depends in part
on a virus-encoded papain-like protease (PLpro) that cleaves the
viral replicase polyproteins at three sites releasing non-structural protein 1
(nsp1), nsp2, and nsp3. In addition to this replicative function, MERS-CoV
PLpro was recently shown to be a deubiquitinating enzyme (DUB)
and to possess deISGylating activity, as previously reported for other
coronaviral PLpro domains, including that of severe acute respiratory
syndrome coronavirus. These activities have been suggested to suppress host
antiviral responses during infection. To understand the molecular basis for
ubiquitin (Ub) recognition and deconjugation by MERS-CoV PLpro, we
determined its crystal structure in complex with Ub. Guided by this structure,
mutations were introduced into PLpro to specifically disrupt Ub
binding without affecting viral polyprotein cleavage, as determined using an in
trans nsp3↓4 cleavage assay. Having developed a
strategy to selectively disable PLpro DUB activity, we were able to
specifically examine the effects of this activity on the innate immune response.
Whereas the wild-type PLpro domain was found to suppress
IFN-β promoter activation, PLpro variants specifically
lacking DUB activity were no longer able to do so. These findings directly
implicate the DUB function of PLpro, and not its proteolytic activity
per se, in the inhibition of IFN-β promoter
activity. The ability to decouple the DUB activity of PLpro from its
role in viral polyprotein processing now provides an approach to further dissect
the role(s) of PLpro as a viral DUB during MERS-CoV infection.
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Affiliation(s)
- Ben A Bailey-Elkin
- From the Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada and
| | - Robert C M Knaap
- the Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Garrett G Johnson
- From the Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada and
| | - Tim J Dalebout
- the Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Dennis K Ninaber
- the Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Puck B van Kasteren
- the Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Peter J Bredenbeek
- the Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Eric J Snijder
- the Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Marjolein Kikkert
- the Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Brian L Mark
- From the Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada and
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